MolNFT v1 · #117886 · protein
Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine
5ELN · Lysine--tRNA ligase: “Crystal structure of lysyl-tRNA synthetase from cryptosporidium parvum complexed with L-lysine”. X-ray diffraction, 1 ligand (LYS), 20 pockets (best druggability 0.83). MolNFT v1 #117886 on GenesisL1: 3D…
- PDB
- 5ELN
- Type
- protein
- Length
- 1,995 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q5CR27
- Ligands
- LYS
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 501 | 36% helix, 26% strand | Q5CR27 |
| C | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 497 | 35% helix, 26% strand | Q5CR27 |
| D | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 496 | 35% helix, 25% strand | Q5CR27 |
Ligands and binding sites
- LYS · Lysine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.83 | 0.88 | 91 | EDO |
| 2 | 311 | 0.81 | 0.91 | 61 | EDO |
| 3 | 817 | 0.80 | 0.83 | 94 | LYS |
| 4 | 825 | 0.79 | 0.82 | 76 | LYS |
| 5 | 830 | 0.79 | 0.82 | 85 | LYS |
Interfaces
4 interfaces between chains.
- A–B · 4390 Ų buried · 62 hydrogen bonds · protein-protein
- C–D · 4382 Ų buried · 62 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ELN · Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5CR27
- Elsewhere: RCSB PDB 5ELN · PDBe 5ELN · UniProt Q5CR27
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